The $2$-cell embeddings of graphs on closed surfaces have been widely studied. It is well known that ($2$-cell) embedding a given graph $G$ on a closed orientable surface is equivalent to cyclically ordering the edges incident to each vertex of $G$. In this paper, we study the following problem: given a genus $g$ embedding $mathbb{E}$ of the graph $G$, if we randomly rearrange the edges around a vertex, i.e., re-embedding, what is the probability of the resulting embedding $mathbb{E}$ having genus $g+Delta g$? We give a formula to compute this probability. Meanwhile, some other known and unknown results are also obtained. For example, we show that the probability of preserving the genus is at least $frac{2}{deg(v)+2}$ for re-embedding any vertex $v$ of degree $deg(v)$ in a one-face embedding; and we obtain a necessary condition for a given embedding of $G$ to be an embedding with the minimum genus.
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These problems are very important in the study of the evolution of genomes. We give a general formulation for lower bounds of the transposition and block-interchange distance from which the existing lower bounds obtained by Bafna and Pevzner, and Christie can be easily derived. As to the reversal distance of signed permutations, we translate it into a block-interchange distance problem of permutations so that we obtain a new lower bound. Furthermore, studying distance problems via our framework motivates several interesting combinatorial problems related to product of permutations, some of which are studied in this paper as well.
In this paper, we introduce plane permutations, i.e. pairs $mathfrak{p}=(s,pi)$ where $s$ is an $n$-cycle and $pi$ is an arbitrary permutation, represented as a two-row array. Accordingly a plane permutation gives rise to three distinct permutations: the permutation induced by the upper horizontal ($s$), the vertical $pi$) and the diagonal ($D_{mathfrak{p}}$) of the array. The latter can also be viewed as the three permutations of a hypermap. In particular, a map corresponds to a plane permutation, in which the diagonal is a fixed point-free involution. We study the transposition action on plane permutations obtained by permuting their diagonal-blocks. We establish basic properties of plane permutations and study transpositions and exceedances and derive various enumerative results. In particular, we prove a recurrence for the number of plane permutations having a fixed diagonal and $k$ cycles in the vertical, generalizing Chapuys recursion for maps filtered by the genus. As applications of this framework, we present a combinatorial proof of a result of Zagier and Stanley, on the number of $n$-cycles $omega$, for which the product $omega(1~2~cdots ~n)$ has exactly $k$ cycles. Furthermore, we integrate studies on the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. Plane permutations allow us to generalize and recover various lower bounds for transposition and block-interchange distances and to connect reversals with block-interchanges.
In this paper we generalize permutations to plane permutations. We employ this framework to derive a combinatorial proof of a result of Zagier and Stanley, that enumerates the number of $n$-cycles $omega$, for which $omega(12cdots n)$ has exactly $k$ cycles. This quantity is $0$, if $n-k$ is odd and $frac{2C(n+1,k)}{n(n+1)}$, otherwise, where $C(n,k)$ is the unsigned Stirling number of the first kind. The proof is facilitated by a natural transposition action on plane permutations which gives rise to various recurrences. Furthermore we study several distance problems of permutations. It turns out that plane permutations allow to study transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. Novel connections between these different distance problems are established via plane permutations.
In this paper we present a topological framework for studying signed permutations and their reversal distance. As a result we can give an alternative approach and interpretation of the Hannenhalli-Pevzner formula for the reversal distance of signed permutations. Our approach utlizes the Poincare dual, upon which reversals act in a particular way and obsoletes the notion of padding of the signed permutations. To this end we construct a bijection between signed permutations and an equivalence class of particular fatgraphs, called $pi$-maps, and analyze the action of reversals on the latter. We show that reversals act via either slicing, gluing or half-flipping of external vertices, which implies that any reversal changes the topological genus by at most one. Finally we revisit the Hannenhalli-Pevzner formula employing orientable and non-orientable, irreducible, $pi$-maps.
Studying the virtual Euler characteristic of the moduli space of curves, Harer and Zagier compute the generating function $C_g(z)$ of unicellular maps of genus $g$. They furthermore identify coefficients, $kappa^{star}_{g}(n)$, which fully determine the series $C_g(z)$. The main result of this paper is a combinatorial interpretation of $kappa^{star}_{g}(n)$. We show that these enumerate a class of unicellular maps, which correspond $1$-to-$2^{2g}$ to a specific type of trees, referred to as O-trees. O-trees are a variant of the C-decorated trees introduced by Chapuy, F{e}ray and Fusy. We exhaustively enumerate the number $s_{g}(n)$ of shapes of genus $g$ with $n$ edges, which is a specific class of unicellular maps with vertex degree at least three. Furthermore we give combinatorial proofs for expressing the generating functions $C_g(z)$ and $S_g(z)$ for unicellular maps and shapes in terms of $kappa^{star}_{g}(n)$, respectively. We then prove a two term recursion for $kappa^{star}_{g}(n)$ and that for any fixed $g$, the sequence ${kappa_{g,t}}_{t=0}^g$ is log-concave, where $kappa^{star}_{g}(n)= kappa_{g,t}$, for $n=2g+t-1$.
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed topological genus there exist only finitely many such shapes. We shall express topological RNA structures as unicellular maps, i.e. graphs together with a cyclic ordering of their half-edges. In this paper we prove a bijection of shapes of topological RNA structures. We furthermore derive a linear time algorithm generating shapes of fixed topological genus. We derive explicit expressions for the coefficients of the generating polynomial of these shapes and the generating function of RNA structures of genus $g$. Furthermore we outline how shapes can be used in order to extract essential information of RNA structure databases.
In this paper we study $gamma$-structures filtered by topological genus. $gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $gamma$-structure is composed by specific building blocks, that have topological genus less than or equal to $gamma$, where composition means concatenation and nesting of such blocks. Our main results are the derivation of a new bivariate generating function for $gamma$-structures via symbolic methods, the singularity analysis of the solutions and a central limit theorem for the distribution of topological genus in $gamma$-structures of given length. In our derivation specific bivariate polynomials play a central role. Their coefficients count particular motifs of fixed topological genus and they are of relevance in the context of genus recursion and novel folding algorithms.
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze the sparsification of a particular decomposition rule, $Lambda^*$, that splits an interval for RNA secondary and pseudoknot structures of fixed topological genus. Essential for quantifying the sparsification is the size of its so called candidate set. We present a combinatorial framework which allows by means of probabilities of irreducible substructures to obtain the expected size of the set of $Lambda^*$-candidates. We compute these expectations for arc-based energy models via energy-filtered generating functions (GF) for RNA secondary structures as well as RNA pseudoknot structures. For RNA secondary structures we also consider a simplified loop-energy model. This combinatorial analysis is then compared to the expected number of $Lambda^*$-candidates obtained from folding mfe-structures. In case of the mfe-folding of RNA secondary structures with a simplified loop energy model our results imply that sparsification provides a reduction of time complexity by a constant factor of 91% (theory) versus a 96% reduction (experiment). For the full loop-energy model there is a reduction of 98% (experiment).
The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting RNAs, called interaction structures, there exist for fixed genus only finitely many irreducible shadows. This implies that for fixed genus there are only finitely many classes of interaction structures. In particular the simplest case of genus zero already provides the formalism for certain types of structures that occur in nature and are not covered by other filtrations. This case of genus zero interaction structures is already of practical interest, is studied here in detail and found to be expressed by a multiple context-free grammar extending the usual one for RNA secondary structures. We show that in $O(n^6)$ time and $O(n^4)$ space complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities.
